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github.com/CellProfiler/CellProfiler-plugins
/ functions
Functions
1,666 in github.com/CellProfiler/CellProfiler-plugins
⨍
Functions
1,666
◇
Types & classes
129
↓ 1 callers
Function
find_max_mode
(list1)
unmaintained_plugins/CellProfiler3/rescale_mode_percentile.py:225
↓ 1 callers
Function
find_max_mode
(list1)
unmaintained_plugins/CellProfiler4_autoconverted/rescalemodepercentile.py:226
↓ 1 callers
Function
find_maxima
Finds local maxima in given image @param image: image for which maxima will be found
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:197
↓ 1 callers
Method
find_seeds
(self, exclude)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:171
↓ 1 callers
Method
find_seeds_from_snakes
Finds seeds from snakes centroids @param snakes: Grown snakes from previous frame @type snakes: list[Snake]
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:157
↓ 1 callers
Method
fit_parameters
:param wait_callback: function that wait and potentially updates UI :param update_callback: function that take number of steps compl
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:841
↓ 1 callers
Method
fit_parameters_with_ui
(self, input_image, background_image, ignore_mask_image, ground_truth_labels)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:898
↓ 1 callers
Method
fit_parameters_with_ui
(self, input_image, background_image, ignore_mask_image, ground_truth_labels)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:901
↓ 1 callers
Function
fourier_transform
(image, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:32
↓ 1 callers
Method
from_ranges
(ranges_dict)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py:37
↓ 1 callers
Method
generate_level_set
Generate a level set based off of the current settings and optionally a specific size. :param shape: Shape of the level set t
unmaintained_plugins/CellProfiler3/activecontourmodel.py:360
↓ 1 callers
Method
generate_level_set
Generate a level set based off of the current settings and optionally a specific size. :param shape: Shape of the level set t
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:362
↓ 1 callers
Function
get_bounding_box
Calculates the minimal bounding box for non zero elements. @returns [ystart,ystop), [xstart,xstop) or None, None
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:56
↓ 1 callers
Method
get_box_boundaries
Calculate the boundary box coordinates for all four sides Parameters: input_label (numpy.array) : internal representatio
active_plugins/boxobjects.py:405
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of labels
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:383
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of lab
unmaintained_plugins/CellProfiler2/calculatehistogram.py:317
↓ 1 callers
Method
get_categories
Get the measurement categories. pipeline - pipeline being run image_name - name of images in question returns a l
unmaintained_plugins/CellProfiler2/calculatemoments.py:327
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of labels
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:382
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of lab
unmaintained_plugins/CellProfiler3/calculatehistogram.py:317
↓ 1 callers
Method
get_categories
Get the measurement categories. pipeline - pipeline being run image_name - name of images in question returns a l
unmaintained_plugins/CellProfiler3/calculatemoments.py:327
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of labels
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:318
↓ 1 callers
Method
get_categories
Get the measurement categories. pipeline - pipeline being run image_name - name of images in question returns a list
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:332
↓ 1 callers
Method
get_categories
Get the measurement categories supplied for the given object name. pipeline - pipeline being run object_name - name of labels in ques
active_plugins/enhancedmeasuretexture.py:434
↓ 1 callers
Method
get_categories
Get the measurement categories. pipeline - pipeline being run image_name - name of images in question returns a list of categ
active_plugins/calculatemoments.py:377
↓ 1 callers
Function
get_confirm_token
(response)
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:320
↓ 1 callers
Function
get_confirm_token
(response)
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:320
↓ 1 callers
Method
get_content_type
(filename)
active_plugins/runvista2d.py:670
↓ 1 callers
Function
get_core
(dim1, dim2)
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:222
↓ 1 callers
Function
get_core
(dim1, dim2)
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:222
↓ 1 callers
Function
get_curvature
(phi, index)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:580
↓ 1 callers
Function
get_curvature
(phi, index)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:582
↓ 1 callers
Method
get_diamond
Get a diamond-shaped structuring element angle - angle at which to tilt the diamond returns a binary array that can be used as a foo
unmaintained_plugins/CellProfiler2/identifylinearobjects.py:315
↓ 1 callers
Method
get_diamond
Get a diamond-shaped structuring element angle - angle at which to tilt the diamond returns a binary array that can be used as a foo
unmaintained_plugins/CellProfiler3/identifylinearobjects.py:315
↓ 1 callers
Method
get_diamond
Get a diamond-shaped structuring element angle - angle at which to tilt the diamond returns a binary array that can be used as a foo
unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py:317
↓ 1 callers
Method
get_feature_name
(self, name)
unmaintained_plugins/CellProfiler3/shollanalysis.py:255
↓ 1 callers
Method
get_feature_name
Return a measurement feature name
unmaintained_plugins/CellProfiler3/measureradialentropy.py:170
↓ 1 callers
Method
get_feature_name
(self, name)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:258
↓ 1 callers
Method
get_feature_name
Return a measurement feature name
unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py:172
↓ 1 callers
Method
get_feature_name_bins
Return a measurement feature name
unmaintained_plugins/CellProfiler3/measureradialentropy.py:174
↓ 1 callers
Method
get_feature_name_bins
Return a measurement feature name
unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py:176
↓ 1 callers
Method
get_filename
(content_disposition)
active_plugins/runvista2d.py:697
↓ 1 callers
Method
get_folder_name
Get original folder name based on user input
active_plugins/boxobjects.py:421
↓ 1 callers
Method
get_measurement_columns
Column definitions for measurements made by IdentifyPrimAutomatic
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:589
↓ 1 callers
Method
get_measurement_columns
(self, pipeline)
unmaintained_plugins/CellProfiler3/measuretrackquality.py:606
↓ 1 callers
Method
get_measurement_columns
(self, pipeline)
unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py:608
↓ 1 callers
Method
get_measurement_columns
(self, pipeline)
active_plugins/callbarcodes.py:815
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured category -
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:412
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured catego
unmaintained_plugins/CellProfiler2/calculatehistogram.py:342
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured category -
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:411
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured catego
unmaintained_plugins/CellProfiler3/calculatehistogram.py:342
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured category -
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:343
↓ 1 callers
Method
get_measurement_images
Get the list of images measured pipeline - pipeline being run object_name - name of objects being measured category - measurem
active_plugins/enhancedmeasuretexture.py:466
↓ 1 callers
Method
get_measurement_objects_name
(self)
unmaintained_plugins/CellProfiler3/thresh_all.py:671
↓ 1 callers
Method
get_measurement_objects_name
(self)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:680
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of objec
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:401
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of ob
unmaintained_plugins/CellProfiler2/calculatehistogram.py:331
↓ 1 callers
Method
get_measurements
Get the measurements made on the given image in the given category pipeline - pipeline being run image_name - name of imag
unmaintained_plugins/CellProfiler2/calculatemoments.py:341
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of objec
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:400
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler3/measureimagefocus.py:89
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of ob
unmaintained_plugins/CellProfiler3/calculatehistogram.py:331
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler3/shollanalysis.py:260
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler3/thresh_all.py:733
↓ 1 callers
Method
get_measurements
Get the measurements made on the given image in the given category pipeline - pipeline being run image_name - name of imag
unmaintained_plugins/CellProfiler3/calculatemoments.py:341
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler4_autoconverted/measureimagefocus.py:93
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of objec
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:332
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:263
↓ 1 callers
Method
get_measurements
Get the measurements made on the given image in the given category pipeline - pipeline being run image_name - name of image b
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:346
↓ 1 callers
Method
get_measurements
(self, pipeline, object_name, category)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:742
↓ 1 callers
Method
get_measurements
Get the measurements made on the given object in the given category pipeline - pipeline being run object_name - name of objects being
active_plugins/enhancedmeasuretexture.py:456
↓ 1 callers
Method
get_measurements
Get the measurements made on the given image in the given category pipeline - pipeline being run image_name - name of image being mea
active_plugins/calculatemoments.py:391
↓ 1 callers
Method
get_medians
(self, X)
unmaintained_plugins/CellProfiler3/compensatecolors.py:477
↓ 1 callers
Method
get_medians
(self, X)
active_plugins/compensatecolors.py:553
↓ 1 callers
Function
get_model_3_class
(dim1, dim2, activation="softmax")
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:288
↓ 1 callers
Function
get_model_3_class
(dim1, dim2, activation="softmax")
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:288
↓ 1 callers
Function
get_object_moment
(pixels, func)
unmaintained_plugins/CellProfiler2/calculatemoments.py:44
↓ 1 callers
Function
get_object_moment
(pixels, func)
unmaintained_plugins/CellProfiler3/calculatemoments.py:44
↓ 1 callers
Function
get_object_moment
(pixels, func)
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:49
↓ 1 callers
Function
get_object_moment
(pixels, labels, func)
active_plugins/calculatemoments.py:52
↓ 1 callers
Function
get_objects_histogram
(pixels, labels, b)
unmaintained_plugins/CellProfiler2/calculatehistogram.py:28
↓ 1 callers
Function
get_objects_histogram
(pixels, labels, b)
unmaintained_plugins/CellProfiler3/calculatehistogram.py:28
↓ 1 callers
Function
get_objects_histogram
(pixels, labels, b)
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:29
↓ 1 callers
Method
get_param_fitting_input_images_from_image_set
Try to load images from current workspace. Can be used when fitting is called in test run after segmentation has been run at least on
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:915
↓ 1 callers
Method
get_param_fitting_input_images_from_image_set
Try to load images from current workspace. Can be used when fitting is called in test run after segmentation has been run at least on
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:918
↓ 1 callers
Method
get_param_fitting_input_images_from_user
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:957
↓ 1 callers
Method
get_param_fitting_input_images_from_user
(self)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:960
↓ 1 callers
Method
get_rectangle
(self, angle)
unmaintained_plugins/CellProfiler2/identifylinearobjects.py:354
↓ 1 callers
Method
get_rectangle
(self, angle)
unmaintained_plugins/CellProfiler3/identifylinearobjects.py:354
↓ 1 callers
Method
get_rectangle
(self, angle)
unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py:356
↓ 1 callers
Function
get_size_weight_list
(params)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:136
↓ 1 callers
Method
get_subfile_name
Contact the UI to find the cellh5 file to use to store results Internally, this tells the UI to create a link from the master file to
unmaintained_plugins/CellProfiler3/exporttocellh5.py:284
↓ 1 callers
Method
get_subfile_name
Contact the UI to find the cellh5 file to use to store results Internally, this tells the UI to create a link from the master file to
unmaintained_plugins/CellProfiler4_autoconverted/exporttocellh5.py:284
↓ 1 callers
Method
getallbarcodemeasurements
(self, measurements, ncycles, examplemeas)
unmaintained_plugins/CellProfiler3/callbarcodes.py:459
↓ 1 callers
Method
getallcyclebarcodemeasurements
(self, measurements, ncycles, examplemeas, object_name)
active_plugins/callbarcodes.py:715
↓ 1 callers
Method
getallonehotbarcodemeasurements
(self, measurements, ncycles, examplemeas)
active_plugins/callbarcodes.py:731
↓ 1 callers
Method
grow
(self, supplementary_parameters=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:57
↓ 1 callers
Function
grow_single_snake
(frame, images, parameters, seed)
unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py:44
↓ 1 callers
Method
grow_snakes
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:186
↓ 1 callers
Method
gt_snake_intersection
(snake, gt)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:92
↓ 1 callers
Function
haar_analysis
(image)
unmaintained_plugins/CellProfiler3/transformfilters.py:289
↓ 1 callers
Function
haar_analysis
(image)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:289
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